Fixing failing tests

carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala

@@ -14,19 +14,19 @@
  */
 package nl.lumc.sasc.biopet.pipelines.carp
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.utils.config.Config
 import nl.lumc.sasc.biopet.extensions.bwa.BwaMem
 import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
-import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.extensions.picard.{MergeSamFiles, SortSam}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ AfterClass, DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 /**
  * Test class for [[Carp]]
@@ -72,6 +72,7 @@ class CarpTest extends TestNGSuite with Matchers {
       intercept[IllegalStateException] {
         initPipeline(map).script()
       }
+      Logging.errors.clear()
     } else { // When samples are correct
       val carp = initPipeline(map)
       carp.script()

gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala

@@ -72,7 +72,7 @@ abstract class GearsTest extends TestNGSuite with Matchers {
     }
 
     if (!sample1 && !sample2) { // When no samples
-      intercept[IllegalArgumentException] {
+      intercept[IllegalStateException] {
         initPipeline(map).script()
       }
       Logging.errors.clear()

mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTest.scala

@@ -14,17 +14,17 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
 import nl.lumc.sasc.biopet.extensions.kraken.Kraken
-import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
 
 /**
  * Created by pjvanthof on 15/05/16.
@@ -72,9 +72,10 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
     }
 
     if (!sample1 && !sample2 && !sample3 && !sample4) { // When no samples
-      intercept[IllegalArgumentException] {
+      intercept[IllegalStateException] {
         initPipeline(map).script()
       }
+      Logging.errors.clear()
     } else if (sample4 && !bamToFastq && !correctReadgroups) {
       intercept[IllegalStateException] {
         initPipeline(map).script()

shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala

@@ -14,18 +14,18 @@
  */
 package nl.lumc.sasc.biopet.pipelines.shiva
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.extensions.gatk.{ BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator }
+import nl.lumc.sasc.biopet.extensions.gatk.{BaseRecalibrator, IndelRealigner, PrintReads, RealignerTargetCreator}
 import nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
 import nl.lumc.sasc.biopet.extensions.tools.VcfStats
-import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.config.Config
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ DataProvider, Test }
+import org.testng.annotations.{DataProvider, Test}
 
 /**
  * Class for testing shiva
@@ -86,6 +86,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
       intercept[IllegalArgumentException] {
         initPipeline(map).script()
       }
+      Logging.errors.clear()
     } else {
       val pipeline = initPipeline(map)
       pipeline.script()